biomaRt error

[GeroKn]

Hi!

Thanks for providing this very helpful package. I'm running into an error with the getEnsemblGenes() function. My code is the following (directly from the vignette):

library(cimpl)
data(colorectal)
library(BSgenome.Mmusculus.UCSC.mm9)
ca <- doCimplAnalysis(colorectal, scales = c(30000, 50000, 70000),chromosomes = c("chr18"), n_iterations = 100, BSgenome = Mmusculus,system = "SB", lhc.method = "none")
genes <- getEnsemblGenes(ca)

It produces this error: Error in getEnsemblGenes(ca) : external_gene_id is/are no valid biomaRt attributes for this mart.

I suppose this is some version incompatibility, but I'm not able to fix the error by accessing an archived mart, they all don't seem to have the attribute "external_gene_id".

I'm using R version 4.4.1 (2024-06-14), biomaRt is 2.60.1 and cimpl is 1.1.

Would be great if you could help me out and please let me know if I need to provide further information.

Best,
Gero

[GeroKn]

From what I've found on the web, "external_gene_id" was changed to "external_gene_name" with version 76. So if I run getEnsemblGenes() with biomaRt version 75, it works:

genes = getEnsemblGenes(ca, mart=useMart("ENSEMBL_MART_ENSEMBL",dataset='mmusculus_gene_ensembl',host='https://feb2014.archive.ensembl.org'))

Probably would still make sense to update the package.

Best!
Gero